This proposal is about phylogenetic origins. Where did cells with nuclei come from and what are the molecular and ultrastructure innovations that permitted their formation? Who were the microbial ancestors to the higher kingdoms of plants, animals and fungi? What are the taxonomic boundaries separating major groups of eukaryotes and how are they interrelated? The answers lie within the kingdom Protista whose members dominated the evolutionary history of eukaryotes. The earliest cells with nuclei and the last common ancestor to plants, animals and fungi were protists, but this taxonomic group is not a cohesive evolutionary assemblage. Instead, it describes levels of organization and is represented by paraphyletic lines of descent that can not be definitively placed in a phylogenetic context using traditional methods of comparative morphology, physiology or biochemistry. Molecular systematics offer a new opportunity to assemble objective, quantitative phylogenies; frameworks that can be used to interpret molecular and structural similarities in divergent taxa, to identify free living relatives to obligate human parasites, and to design diagnostic rRNA probes for identification of pathogens. During the past few years, comparisons of ribosomal RNA coding regions have revolutionized our perspective on eukaryotic evolution. Instead of three "higher kingdoms", there are five major complex evolutionary assemblages that diverged nearly simultaneously and relatively late in the evolutionary history of the eukaryotic line of descent. The massive phyletic radiation was preceded by a progression of independent protist lineages; some as ancient as the archaebacterial and eubacterial lines of descent. The earliest branches are represented by amitochondrial parasites, many of which cause disease in humans. However information about the deepest eukaryotic branching patterns is minimal and it is not yet possible to identify the order of separation for the major eukaryotic groups. The goal of this proposal is construct a quantitative phylogenetic framework for eukaryotes based upon comparisons of small subunit ribosomal RNA gene sequences.